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epiflows 0.1

Changes to class

• epiflows class inherits the epicontacts class. This class is built from two data frames describing a linlist (referred here as locations) and contacts (referred here as flows). This was chosen over the previous implementation of two named vectors of inward and outward flows with a data frame of locations to allow the user to flexibly store more than one focus. An extra element called vars has been added, storing a dictionary of variables that are present in the data frame for use with estimate_risk_spread(). These variables are accessible via global_vars()

Changes to estimate_risk_spread

• The function is now a generic with a default and an epiflows method.
• The number of options have been reduced by combining the function and parameter arguments into one.
• All errors are collected and reported if multiple arguments are missing or misspelled
• Default varaibles have been set
• a new parameter, return_all_simulations has been added.

Changes to constructor

• make_epiflows() is now a generic with methods for data frame, integer, and numeric input.

Changes to plotting

• plot() defaults to an interactive network plot from visNetwork() if no coordinates are available.
• map_epiflows() places flows on a map
• vis_epiflows() places flows on a network
• grid_epiflows() places flows on a bubble plot/grid

New functions

• get_flows() returns the flows data frame optionally specifying flows from/to a given location
• get_locations() returns the locations data frame
• get_coordinates() returns coordinates or NULL from the locations data frame
• get_id() returns the identifier of all locations
• get_n() returns a numeric vector of cases from/to a given location
• get_pop_size() returns a vector of population sizes for locations
• get_vars() returns a specified variable from the locations data frame OR returns the defined variables if no arguments are given.
• set_vars() allows the user to set or reset the global variables.
• global_vars() can return, set, and reset globally recognized variables
• as.SpatialLinesDataFrame() converts an epiflows object with coordinates to a SpatialLinesDataFrame class from the sp package.

New data sets

• Brazil_epiflows is an epiflows object created from the YF_Brazil data
• YF_flows is the data frame of flows from YF_Brazil
• YF_locations is the data frame of locations from YF_Brazil
• YF_coordinates are the coordinates for the locations in YF_Brazil

Removed functions/data

• get_codes() has been removed in favor of get_id()
• get_flow_data() has been removed in favor of get_n() and get_flows()
• get_location_data() has been removed in favor of get_locations()
• Mex_travel_2009 has been removed

Misc

• add_coordinates() can now take a data frame input
• Magrittr pipes are no longer imported.
• visNetwork is imported
• vdiffr is used for visual tests
• continuous integration and automated tests have been set up
• A new vignette describing the epiflows class has been added
• README and introduction vignette have been updated.

epiflows 0.0.1.9000

• Added a NEWS.md file to track changes to the package.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.